[RTM] HMC refactor around non-steady state #421
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Contributor
chrisgorgo
commented
Apr 1, 2017
chrisgorgo
commented
- Non-steady state detector was added to HMC workflow
- Reference image estimator for HMC was added:
- If non-steady state is detected it will be used as a reference (they tend to have better tissue contrast)
- Otherwise a median of 20 motion corrected volumes will be used as a reference
- EPI skull mask reportlet was brought back
chrisgorgo
changed the title
oesteban
approved these changes
Apr 3, 2017
docs/workflows.rst
Outdated
| line argument. | ||
|
|
||
| FSL MCFLIRT is used to estimate motion | ||
| transformations using a automatically estimated reference scan. If T1-saturation effects |
| else: | ||
| slice_fname = self.inputs.in_file | ||
|
|
||
| res = Volreg(in_file=slice_fname, args='-Fourier -twopass', zpad=4, |
There was a problem hiding this comment.
Why not mcflirt here again? (just a question, I assume 3dvolreg works better here)
There was a problem hiding this comment.
I trust AFNIs interpolation more.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.